1)
What is the meaning of "Kamah Yamruhu va'Midbar"?
1.
Rashi: They often rebelled against Him in the Midbar 1 (Radak - other than what is mentioned [in the Torah]) They angered Him via deviating from His Mitzvos.
1
Malbim: E.g. ha'Egel, Korach and Beis Pe'or.
2)
Why does it say "Ya'atzivuhu bi'Yshimon"?
1.
Radak: The matter is repeated in different words.
2.
Malbim: They saddened him because the Midbar was Yeshimon (desolate); they complained about the manna and lack of water.